Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.

Using density-functional theory they found that, depending on coverage, coadsorbed oxygen can act both as a promoter and as an inhibitor of the dissociation of water on Ru(0001), the transition between these two behaviors occurring at (0.2 M). The key factor that determines this transition is the adsorption energy of the reaction products, OH in particular. The chemistry of this coadsorbed system is dictated by the effective coordination of the Ru atoms that participate in the bonding of the different species. In particular, they observed that a low coverage of oxygen increases the adsorption energy of the OH fraction on the Ru surface. This surprising extra stabilization of the OH with the coadsorption of oxygen can be understood in the context of the metallic bonding and could well correspond to a general trend for the coadsorption of electronegative species on metallic surfaces.

Corrosion of steel canisters, stored in a repository for spent fuel and high-level nuclear wastes, leads to the generation and accumulation of hydrogen gas in the backfilled emplacement tunnels, which may significantly affect long-term repository safety. Previous studies used H{sub 2} generation rates based on the volume of the waste or canister material and the stoichiometry of the corrosion reaction. However, iron corrosion and H{sub 2} generation rates vary with time, depending on factors such as amount of iron, water availability, water contact area, and aqueous and solid chemistry. To account for these factors and feedback mechanisms, we developed a chemistry model related to iron corrosion, coupled with two-phase (liquid and gas) flow phenomena that are driven by gas-pressure buildup associated with H{sub 2} generation and water consumption. Results indicate that by dynamically calculating H{sub 2} generation rates based on a simple model of corrosion chemistry, and by coupling this corrosion reaction with two-phase flow processes, the degree and extent of gas pressure buildup could be much smaller compared to a model that neglects the coupling between flow and reactive transport mechanisms. By considering the feedback of corrosion chemistry, the gas pressure increases initially at the canister, but later decreases …

Amorphous titania (TiO{sub 2}) is an important precursor for synthesis of single-phase nanocrystalline anatase. We synthesized x-ray amorphous titania by hydrolysis of titanium ethoxide at the ice point. Transmission electron microscopy examination and nitrogen gas adsorption indicated the particle size of the synthesized titania is {approx} 2 nm. Synchrotron wide-angle x-ray scattering (WAXS) was used to probe the atomic correlations in this amorphous sample. Atomic pair-distribution function (PDF) derived from Fourier transform of the WAXS data was used for reverse Monte Carlo (RMC) simulations of the atomic structure of the amorphous TiO{sub 2} nanoparticles. Molecular dynamics simulations were used to generate input structures for the RMC. X-ray absorption spectroscopy (XAS) simulations were used to screen candidate structures obtained from the RMC by comparing with experimental XAS data. The structure model that best describes both the WAXS and XAS data shows that an amorphous TiO{sub 2} particle consists of a highly distorted shell and a small strained anatase-like crystalline core. The average coordination number of Ti is 5.3 and most Ti-O bonds are populated around 1.940 {angstrom}. Relative to bulk TiO{sub 2}, the reduction of the coordination number is primarily due to the truncation of the Ti-O octahedra at the amorphous …

Recent CO{sub 2} sequestration pilot projects have implemented novel approaches to well-based subsurface monitoring aimed at increasing the amount and quality of information available from boreholes. Some of the drivers for the establishment of new well-based technologies and methodologies arise from: (1) the need for data to assess physical and geochemical subsurface processes associated with CO{sub 2} emplacement; (2) the high cost of deep boreholes and need to maximize data yield from each; (3) need for increased temporal resolution to observe plume evolution; (4) a lack of established processes and technologies for integrated permanent sensors in the oil and gas industry; and (5) a lack of regulatory guidance concerning the amount, type, and duration of monitoring required for long-term performance confirmation of a CO{sub 2} storage site. In this paper we will examine some of the latest innovations in well-based monitoring and present examples of integrated monitoring programs.

Possible means of reducing atmospheric CO{sub 2} emissions include injecting CO{sub 2} in petroleum reservoirs for Enhanced Oil Recovery or storing CO{sub 2} in deep saline aquifers. Large-scale injection of CO{sub 2} into subsurface reservoirs would induce a complex interplay of multiphase flow, capillary trapping, dissolution, diffusion, convection, and chemical reactions that may have significant impacts on both short-term injection performance and long-term fate of CO{sub 2} storage. Reactive Transport Modeling is a promising approach that can be used to predict the spatial and temporal evolution of injected CO{sub 2} and associated gas-fluid-rock interactions. This presentation will summarize recent advances in reactive transport modeling of CO{sub 2} storage and review key technical issues on (1) the short- and long-term behavior of injected CO{sub 2} in geological formations; (2) the role of reservoir mineral heterogeneity on injection performance and storage security; (3) the effect of gas mixtures (e.g., H{sub 2}S and SO{sub 2}) on CO{sub 2} storage; and (4) the physical and chemical processes during potential leakage of CO{sub 2} from the primary storage reservoir. Simulation results suggest that CO{sub 2} trapping capacity, rate, and impact on reservoir rocks depend on primary mineral composition and injecting gas mixtures. For example, models …

The construction of a host of interesting patterns over one and two dimensions, as transformations of multifractal measures via fractal interpolating functions related to simple affine mappings, is reviewed. It is illustrated that, while space-filling fractal functions most commonly yield limiting Gaussian distribution measures (bells), there are also situations (depending on the affine mappings parameters) in which there is no limit. Specifically, the one-dimensional case may result in oscillations between two bells, whereas the two-dimensional case may give rise to unexpected circle map dynamics of an arbitrary number of two-dimensional circular bells. It is also shown that, despite the multitude of bells over two dimensions, whose means dance making regular polygons or stars inscribed on a circle, the iteration of affine maps yields exotic kaleidoscopes that decompose such an oscillatory pattern in a way that is similar to the many cases that converge to a single bell.

We present the extension of a deterministic fractal geometric procedure aimed at representing the complexity of the spatio-temporal patterns encountered in environmental applications. The original procedure, which is based on transformations of multifractal distributions via fractal functions, is extended through the introduction of nonlinear perturbations to the underlying iterated linear maps. We demonstrate how the nonlinear perturbations generate yet a richer collection of patterns by means of various simulations that include evolutions of patterns based on changes in their parameters and in their statistical and multifractal properties. It is shown that the nonlinear extensions yield structures that closely resemble complex hydrologic temporal data sets, such as rainfall and runoff time series, and width-functions of river networks as a function of distance from the basin outlet. The implications of this nonlinear approach for environmental modeling and prediction are discussed.

During the construction and operational phases of a high-level radioactive waste (HLW) repository constructed in a clay formation, ventilation of underground drifts will cause desaturation and oxidation of the rock. The Ventilation Experiment (VE) was performed in a 1.3 m diameter unlined horizontal microtunnel on Opalinus clay at Mont Terri underground research laboratory in Switzerland to evaluate the impact of desaturation on rock properties. A multiphase flow and reactive transport model of VE is presented here. The model accounts for liquid, vapor and air flow, evaporation/condensation and multicomponent reactive solute transport with kinetic dissolution of pyrite and siderite and local-equilibrium dissolution/precipitation of calcite, ferrihydrite, dolomite, gypsum and quartz. Model results reproduce measured vapor flow, liquid pressure and hydrochemical data and capture the trends of measured relative humidities, although such data are slightly overestimated near the rock interface due to uncertainties in the turbulence factor. Rock desaturation allows oxygen to diffuse into the rock and triggers pyrite oxidation, dissolution of calcite and siderite, precipitation of ferrihydrite, dolomite and gypsum and cation exchange. pH in the unsaturated rock varies from 7.8 to 8 and is buffered by calcite. Computed changes in the porosity and the permeability of Opalinus clay in the unsaturated …

In this paper a method for the estimation of the curvature along a condensed phase interface is presented. In a previous paper in this journal [1] a mathematical relationship was established between this curvature and a template disk located at a given point along the interface. The portion of the computed area of the template disk covering one of the phases was shown to be asymptotically linear in the mean curvature. Instead of utilizing this relationship, an empirical approach was proposed in [1] in order to compensate for discrete uncertainties. In this paper, we show that this linear relationship can be used directly along the interface avoiding the empirical approach proposed earlier. Modifications of the algorithm are however needed, and with good data smoothing techniques, our method provides good quantitative curvature estimates.